Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58.
Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58.
复制标题
植物病原菌基因组农杆菌C58菌株蛋白编码基因的理论预测和实验验证。
DOI：
10.1371/journal.pone.0043176
复制
发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Chen LL
中科院分区：
文献类型：
--
作者：
Wang Q;Lei Y;Xu X;Wang G;Chen LL
根癌农杆菌C58菌株是一种革兰氏阴性土壤细菌，能在许多双子叶植物上诱导肿瘤(冠瘤)。利用Z曲线方法对根癌农杆菌C58菌株的基因组进行了重新注释。首先，对所有的“假设基因”进行了重新鉴定，其中29个最初被注释的“假设基因”被确认为非编码开放阅读框架(ORF)。从主成分分析、蛋白质占据的同源基团簇和平均长度分布获得的理论证据表明，这些非编码ORF极不可能编码蛋白质。对根癌农杆菌C58三个不同生长阶段的逆转录-聚合酶链式反应(RT-PCR)实验结果证实，在已鉴定的非编码ORF中，有23个(79%)在这三个生长阶段没有转录本。此外，通过理论预测，19个潜在的蛋白质编码基因被预测为新的蛋白质编码基因。这些基因中有15个(79%)被RT-PCR实验验证。RT-PCR实验结果证实了我们的理论预测的可靠性，表明在根癌农杆菌C58基因组的注释中总是存在假阳性预测和基因缺失。改进后的注释将为研究根癌农杆菌C58的生活方式、代谢和致病性提供有价值的资源。根癌农杆菌C58的重新注释可从http://211.69.128.148/Atum/.获得
Agrobacterium tumefaciens strain C58 is a Gram-negative soil bacterium capable of inducing tumors (crown galls) on many dicotyledonous plants. The genome of A. tumefaciens strain C58 was re-annotated based on the Z-curve method. First, all the ‘hypothetical genes’ were re-identified, and 29 originally annotated ‘hypothetical genes’ were recognized to be non-coding open reading frames (ORFs). Theoretical evidence obtained from principal component analysis, clusters of orthologous groups of proteins occupation, and average length distribution showed that these non-coding ORFs were highly unlikely to encode proteins. Results from the reverse transcription-polymerase chain reaction (RT-PCR) experiments on three different growth stages of A. tumefaciens C58 confirmed that 23 (79%) of the identified non-coding ORFs have no transcripts in these growth stages. In addition, using theoretical prediction, 19 potential protein-coding genes were predicted to be new protein-coding genes. Fifteen (79%) of these genes were verified with RT-PCR experiments. The RT-PCR experimental results confirmed the reliability of our theoretical prediction, indicating that false-positive prediction and missing genes always exist in the annotation of A. tumefaciens C58 genome. The improved annotation will serve as a valuable resource for the research of the lifestyle, metabolism, and pathogenicity of A. tumefaciens C58. The re-annotation of A. tumefaciens C58 can be obtained from http://211.69.128.148/Atum/.